Charged Carboxyl Group... bond to O- missing

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Charged Carboxyl Group... bond to O- missing #22104 09/17/09 12:35 PM
Joined: Feb 2009 Posts: 83 B blubbi OP Forum Member
OP blubbi Forum Member B Joined: Feb 2009 Posts: 83	Hi again, can anybody tell me if this toppar is correct? I doubt it, cause VMD only shows a bond to O1 but not to O2. I can't figure out where the mistake is hiding The rest of the molecule is generated correctly. Code: * BA residue * GROUP ! O1 O2 (-) ATOM C1 CL 0.62 ! \\ / ATOM O1 OCL -0.76 ! C1 ATOM O2 OCL -0.76 ! \| ATOM C2 CTL2 -0.28 ! \| ATOM H2A HAL2 0.09 ! H2A---C2---H2B [...] ! bonding BOND C1 C2 C1 O1 C1 O2 [...] DOUBLE C1 O1 ACCEPTOR 01 C1 ACCEPTOR 02 C1 ! chain torsions IC O1 C1 C2 C3 0.0 0.0 180.0 0.0 0.0 IC O2 C1 C2 C3 0.0 0.0 0.0 0.0 0.0 [...] Thanks and kind regards Bjoern

Re: Charged Carboxyl Group... bond to O- missing blubbi #22110 09/17/09 05:05 PM
Joined: Sep 2003 Posts: 8,650 Likes: 26 39 59 56 N, 77 06 07 W rmv Forum Member
rmv Forum Member Joined: Sep 2003 Posts: 8,650 Likes: 26 39 59 56 N, 77 06 07 W	Unless you importing PSF+CRD, I wouldn't rely on what VMD draws to validate connectivity. I believe that specifying the C1 O1 pair in both a BOND and a DOUBLE statement is redundant; I'm surprised that CHARMM does not complain about that. You may also be missing an IMPR energy term for the planarity of the carboxylate anion; the abbreviated post makes it hard to tell. This is really a question for the Parameter Set forum ... Rick Venable computational chemist

Re: Charged Carboxyl Group... bond to O- missing

rmv #22118 09/18/09 08:12 AM

Joined: Feb 2009

Posts: 83

blubbi

Forum Member

blubbi

Forum Member

Joined: Feb 2009

Posts: 83

Originally Posted By: rmv

Unless you importing PSF+CRD, I wouldn't rely on what VMD draws to validate connectivity.

I did import the PSF+CRD, cause I don't wanted to rely on the PDB without connect records.

Originally Posted By: rmv

I believe that specifying the C1 O1 pair in both a BOND and a DOUBLE statement is redundant; I'm surprised that CHARMM does not complain about that.

Okay, the DOUBLE was just a try to see if it somehow helps, but with our without DOUBLE, the connection to O2 is missing

Originally Posted By: rmv

You may also be missing an IMPR energy term for the planarity of the carboxylate anion; the abbreviated post makes it hard to tell.

Adding "IMPR C1 C2 O2 O1" like in GLU didn't makes the O2 disappear completely.

Originally Posted By: rmv

This is really a question for the Parameter Set forum ...

Can someone move it?

Sory for the waves, I found the mistake, or at least I think so. With the toppar below I get a working PSF/CRD combination. Anyway, RMV would you mind to countercheck that toppar regarding the IMPR?

This is the command sequence I used to generate the molecule:

Code:

*Test for BA
*

open read card unit 10 name top_all32_lipid_prot_cmap.rtf
read  rtf card unit 10
close unit 10

open read card unit 20 name par_all32_lipid_prot_cmap.prm
read para card unit 20
close unit 20

bomlev -1
stream toppar_add_ba.str
bomlev 0

!BUILD FIRST BA MOLECULE
read sequence BA 1
generate BA setup first none last none
autogen angle dihedrals
ic param
ic seed BA 1 O1 BA 1 C1 BA 1 C2
ic build
!NBONDS CUTNB 10
hbuild

open write card unit 1 name lipids-only.psf
write psf card unit 1

open write card unit 1 name lipids-only.xplor.psf
write psf card unit 1 xplor

open write card unit 1 name lipids-only.pdb
write coor pdb unit 1

open write card unit 1 name lipids-only.cor
write coor card unit 1

stop

Please find attached the output (ba.txt) and the CRD and PSF file for BA.

Here's the full toppar:

Code:

* Toppar stream file for BA.  Stream following reading of
* top_all32_lipid_prot_cmap.rtf
* and
* par_all32_lipid_prot_cmap.prm
*

read rtf card append
* BA residue
*

RESI BA         -1.00 ! docosanoic acid (C22)
GROUP                 !      O1  O2 (-)
ATOM C1   CL     0.62 !       \\ /
ATOM O1   OCL   -0.76 !        C1
ATOM O2   OCL   -0.76 !         |
ATOM C2   CTL2  -0.28 !         |
ATOM H2A  HAL2   0.09 !   H2A---C2---H2B
ATOM H2B  HAL2   0.09 !         |
GROUP                 !
ATOM C3   CTL2  -0.18 !         |
ATOM H3A  HAL2   0.09 !   H3A---C3---H3B
ATOM H3B  HAL2   0.09 !         |
GROUP                 !
ATOM C4   CTL2  -0.18 !         |
ATOM H4A  HAL2   0.09 !   H4A---C4---H4B
ATOM H4B  HAL2   0.09 !         |
GROUP                 !
ATOM C5   CTL2  -0.18 !         |
ATOM H5A  HAL2   0.09 !   H5A---C5---H5B
ATOM H5B  HAL2   0.09 !         |
GROUP                 !
ATOM C6   CTL2  -0.18 !         |
ATOM H6A  HAL2   0.09 !   H6A---C6---H6B
ATOM H6B  HAL2   0.09 !         |
GROUP                 !
ATOM C7   CTL2  -0.18 !         |
ATOM H7A  HAL2   0.09 !   H7A---C7---H7B
ATOM H7B  HAL2   0.09 !         |
GROUP                 !
ATOM C8   CTL2  -0.18 !         |
ATOM H8A  HAL2   0.09 !   H8A---C8---H8B
ATOM H8B  HAL2   0.09 !         |
GROUP                 !
ATOM C9   CTL2  -0.18 !         |
ATOM H9A  HAL2   0.09 !   H9A---C9---H9B
ATOM H9B  HAL2   0.09 !         |
GROUP                 !
ATOM C10  CTL2  -0.18 !         |
ATOM H10A HAL2   0.09 !  H10A---C10---H10B
ATOM H10B HAL2   0.09 !         |
GROUP                 !
ATOM C11  CTL2  -0.18 !         |
ATOM H11A HAL2   0.09 !  H11A---C11--H11B
ATOM H11B HAL2   0.09 !         |
GROUP                 !
ATOM C12  CTL2  -0.18 !         |
ATOM H12A HAL2   0.09 !  H12A---C12--H12B
ATOM H12B HAL2   0.09 !         |
GROUP                 !
ATOM C13  CTL2  -0.18 !         |
ATOM H13A HAL2   0.09 !  H13A---C13--H13B
ATOM H13B HAL2   0.09 !         |
GROUP                 !
ATOM C14  CTL2  -0.18 !         |
ATOM H14A HAL2   0.09 !  H14A---C14--H14B
ATOM H14B HAL2   0.09 !         |
GROUP                 !
ATOM C15  CTL2  -0.18 !         |
ATOM H15A HAL2   0.09 !  H15A---C15--H15B
ATOM H15B HAL2   0.09 !         |
GROUP
ATOM C16  CTL2  -0.18 !         |
ATOM H16A HAL2   0.09 !  H16A---C16--H16B
ATOM H16B HAL2   0.09 !         |
GROUP                 !
ATOM C17  CTL2  -0.18 !         |
ATOM H17A HAL2   0.09 !  H17A---C17--H17B
ATOM H17B HAL2   0.09 !         |
GROUP                 !
ATOM C18  CTL2  -0.18 !         |
ATOM H18A HAL2   0.09 !  H18A---C18--H18B
ATOM H18B HAL2   0.09 !         |
GROUP                 !
ATOM C19  CTL2  -0.18 !         |
ATOM H19A HAL2   0.09 !  H19A---C19--H19B
ATOM H19B HAL2   0.09 !         |
GROUP                 !
ATOM C20  CTL2  -0.18 !         |
ATOM H20A HAL2   0.09 !  H20A---C20--H20B
ATOM H20B HAL2   0.09 !         |
GROUP                 !
ATOM C21  CTL2  -0.18 !         |
ATOM H21A HAL2   0.09 !  H21A---C21--H21B
ATOM H21B HAL2   0.09 !         |
GROUP                 !
ATOM C22  CTL3  -0.27 !         |
ATOM H22A HAL3   0.09 !  H22A---C22--H22B
ATOM H22B HAL3   0.09 !         |
ATOM H22C HAL3   0.09 !         H22C
! bonding
BOND  C1  O1     C1  C2      C1  O2
BOND  C2  C3     C2  H2A     C2  H2B
BOND  C3  C4     C3  H3A     C3  H3B
BOND  C4  C5     C4  H4A     C4  H4B
BOND  C5  C6     C5  H5A     C5  H5B
BOND  C6  C7     C6  H6A     C6  H6B
BOND  C7  C8     C7  H7A     C7  H7B
BOND  C8  C9     C8  H8A     C8  H8B
BOND  C9  C10    C9  H9A     C9  H9B
BOND  C10 C11    C10 H10A    C10 H10B
BOND  C11 C12    C11 H11A    C11 H11B
BOND  C12 C13    C12 H12A    C12 H12B
BOND  C13 C14    C13 H13A    C13 H13B
BOND  C14 C15    C14 H14A    C14 H14B
BOND  C15 C16    C15 H15A    C15 H15B
BOND  C16 C17    C16 H16A    C16 H16B
BOND  C17 C18    C17 H17A    C17 H17B
BOND  C18 C19    C18 H18A    C18 H18B
BOND  C19 C20    C19 H19A    C19 H19B
BOND  C20 C21    C20 H20A    C20 H20B
BOND  C21 C22    C21 H21A    C21 H21B
BOND  C22 H22C   C22 H22A    C22 H22B
! chain torsions
IC       O1   C1   C2   C3    0.0  0.0  180.0  0.0  0.0
IC       O2   C1   C2   C3    0.0  0.0    0.0  0.0  0.0
IC       C1   C2   C3   C4    0.0  0.0  180.0  0.0  0.0
IC       C2   C3   C4   C5    0.0  0.0  180.0  0.0  0.0
IC       C3   C4   C5   C6    0.0  0.0  180.0  0.0  0.0
IC       C4   C5   C6   C7    0.0  0.0  180.0  0.0  0.0
IC       C5   C6   C7   C8    0.0  0.0  180.0  0.0  0.0
IC       C6   C7   C8   C9    0.0  0.0  180.0  0.0  0.0
IC       C7   C8   C9   C10   0.0  0.0  180.0  0.0  0.0
IC       C8   C9   C10  C11   0.0  0.0  180.0  0.0  0.0
IC       C9   C10  C11  C12   0.0  0.0  180.0  0.0  0.0
IC       C10  C11  C12  C13   0.0  0.0  180.0  0.0  0.0
IC       C11  C12  C13  C14   0.0  0.0  180.0  0.0  0.0
IC       C12  C13  C14  C15   0.0  0.0  180.0  0.0  0.0
IC       C13  C14  C15  C16   0.0  0.0  180.0  0.0  0.0
IC       C14  C15  C16  C17   0.0  0.0  180.0  0.0  0.0
IC       C15  C16  C17  C18   0.0  0.0  180.0  0.0  0.0
IC       C16  C17  C18  C19   0.0  0.0  180.0  0.0  0.0
IC       C17  C18  C19  C20   0.0  0.0  180.0  0.0  0.0
IC       C18  C19  C20  C21   0.0  0.0  180.0  0.0  0.0
IC       C19  C20  C21  C22   0.0  0.0  180.0  0.0  0.0
! impropers (from toplip.rtf ...)
IC H2A  C1  *C2  C3    0.0000  0.00   120.00  0.00  0.0000
IC H2B  C1  *C2  C3    0.0000  0.00  -120.00  0.00  0.0000
IC H3A  C2  *C3  C4    0.0000  0.00   120.00  0.00  0.0000
IC H3B  C2  *C3  C4    0.0000  0.00  -120.00  0.00  0.0000
IC H4A  C3  *C4  C5    0.0000  0.00   120.00  0.00  0.0000
IC H4B  C3  *C4  C5    0.0000  0.00  -120.00  0.00  0.0000
IC H5A  C4  *C5  C6    0.0000  0.00   120.00  0.00  0.0000
IC H5B  C4  *C5  C6    0.0000  0.00  -120.00  0.00  0.0000
IC H6A  C5  *C6  C7    0.0000  0.00   120.00  0.00  0.0000
IC H6B  C5  *C6  C7    0.0000  0.00  -120.00  0.00  0.0000
IC H7A  C6  *C7  C8    0.0000  0.00   120.00  0.00  0.0000
IC H7B  C6  *C7  C8    0.0000  0.00  -120.00  0.00  0.0000
IC H8A  C7  *C8  C9    0.0000  0.00   120.00  0.00  0.0000
IC H8B  C7  *C8  C9    0.0000  0.00  -120.00  0.00  0.0000
IC H9A  C8  *C9  C10   0.0000  0.00   120.00  0.00  0.0000
IC H9B  C8  *C9  C10   0.0000  0.00  -120.00  0.00  0.0000
IC H10A C9  *C10 C11   0.0000  0.00   120.00  0.00  0.0000
IC H10B C9  *C10 C11   0.0000  0.00  -120.00  0.00  0.0000
IC H11A C10 *C11 C12   0.0000  0.00   120.00  0.00  0.0000
IC H11B C10 *C11 C12   0.0000  0.00  -120.00  0.00  0.0000
IC H12A C11 *C12 C13   0.0000  0.00   120.00  0.00  0.0000
IC H12B C11 *C12 C13   0.0000  0.00  -120.00  0.00  0.0000
IC H13A C12 *C13 C14   0.0000  0.00   120.00  0.00  0.0000
IC H13B C12 *C13 C14   0.0000  0.00  -120.00  0.00  0.0000
IC H14A C13 *C14 C15   0.0000  0.00   120.00  0.00  0.0000
IC H14B C13 *C14 C15   0.0000  0.00  -120.00  0.00  0.0000
IC H15A C14 *C15 C16   0.0000  0.00   120.00  0.00  0.0000
IC H15B C14 *C15 C16   0.0000  0.00  -120.00  0.00  0.0000
IC H16A C15 *C16 C17   0.0000  0.00   120.00  0.00  0.0000
IC H16B C15 *C16 C17   0.0000  0.00  -120.00  0.00  0.0000
IC H17A C16 *C17 C18   0.0000  0.00   120.00  0.00  0.0000
IC H17B C16 *C17 C18   0.0000  0.00  -120.00  0.00  0.0000
IC H18A C17 *C18 C19   0.0000  0.00   120.00  0.00  0.0000
IC H18B C17 *C18 C19   0.0000  0.00  -120.00  0.00  0.0000
IC H19A C18 *C19 C20   0.0000  0.00   120.00  0.00  0.0000
IC H19B C18 *C19 C20   0.0000  0.00  -120.00  0.00  0.0000
IC H20A C19 *C20 C21   0.0000  0.00   120.00  0.00  0.0000
IC H20B C19 *C20 C21   0.0000  0.00  -120.00  0.00  0.0000
IC H21A C20 *C21 C22   0.0000  0.00   120.00  0.00  0.0000
IC H21B C20 *C21 C22   0.0000  0.00  -120.00  0.00  0.0000
IC C20  C21  C22 H22A  0.0000  0.00   180.00  0.00  0.0000
IC H22A C21 *C22 H22B  0.0000  0.00   120.00  0.00  0.0000
IC H22A C21 *C22 H22C  0.0000  0.00  -120.00  0.00  0.0000
end

return

Attached Images

ba.inp.txt (687 Bytes, 291 downloads)

ba.out.txt (7.43 KB, 280 downloads)

ba.crd (4.73 KB, 226 downloads)

ba.psf (18.54 KB, 208 downloads)

Last edited by blubbi; 09/18/09 08:19 AM.

Re: Charged Carboxyl Group... bond to O- missing blubbi #22124 09/18/09 04:29 PM
Joined: Sep 2003 Posts: 8,650 Likes: 26 39 59 56 N, 77 06 07 W rmv Forum Member
rmv Forum Member Joined: Sep 2003 Posts: 8,650 Likes: 26 39 59 56 N, 77 06 07 W	Have a look at the PALM residue in top_all27_lipid.rtf Rick Venable computational chemist

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CHARMM Development Project Forums User Discussion & Questions Setup, I/O, and Basic questions Charged Carboxyl Group... bond to O- missing